theAbysmal Shape of Time

18 December 2016

If only I knew how to CGI.

I imagine, if I were able to animate theAbysmal Calendar as a visualization, I would begin with a string of days. Each day would be represented by a sphere, and they would stretch off ahead and backwards indefinitely. If you chose to look at the lunar cycles, then the days would form loops of 29 or 30 days out of the line. If we tie those to the year, the there are 12 or 13 of those loops for every year. If we measure the Metonic Cycle, then there’s another loop every 19 years.

That’s one example.  theAbysmal would be highly variable within the year, however, if we organize our year as the Maya by orders of 20, we get 20 day loop, 18 of those in a year (minus 5 leap days), then 20 years, 400 years, 8000, 160000, etc. It would be a similar effect to DNA supercoiling. A coil made up of coils made up of coils made up of…

And if theAbysmal behaves like DNA in this respect, in what other ways can they be linked?

mycelium - theAbysmal Color


DNA animations

26 August 2012

The wonders of DNA and computing continue.

Back in the day, some decades back, I could have used the following video when I was studying biology. Static pictures were only so helpful when it came to describing the supercoiling and replication.

here’s an earlier one.

117 Days to Dec 21st 2012


Biological Computing

25 August 2012

DNA computers, organs and electronic interface.

DNA computing takes another leap forward, and the interface between man and machine gets one step closer to wetware.

Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

A bioengineer and geneticist at Harvard’s Wyss Institute have successfully stored 5.5 petabits of data — around 700 terabytes — in a single gram of DNA, smashing the previous DNA data density record by a thousand times.

The work, carried out by George Church and Sri Kosuri, basically treats DNA as just another digital storage device. Instead of binary data being encoded as magnetic regions on a hard drive platter, strands of DNA that store 96 bits are synthesized, with each of the bases (TGAC) representing a binary value (T and G = 1, A and C = 0).

To read the data stored in DNA, you simply sequence it — just as if you were sequencing the human genome — and convert each of the TGAC bases back into binary. To aid with sequencing, each strand of DNA has a 19-bit address block at the start (the red bits in the image below) — so a whole vat of DNA can be sequenced out of order, and then sorted into usable data using the addresses.

Scientists have been eyeing up DNA as a potential storage medium for a long time, for three very good reasons: It’s incredibly dense (you can store one bit per base, and a base is only a few atoms large); it’s volumetric (beaker) rather than planar (hard disk); and it’s incredibly stable — where other bleeding-edge storage mediums need to be kept in sub-zero vacuums, DNA can survive for hundreds of thousands of years in a box in your garage.

It is only with recent advances in microfluidics and labs-on-a-chip that synthesizing and sequencing DNA has become an everyday task, though. While it took years for the original Human Genome Project to analyze a single human genome (some 3 billion DNA base pairs), modern lab equipment with microfluidic chips can do it in hours. Now this isn’t to say that Church and Kosuri’s DNA storage is fast — but it’s fast enough for very-long-term archival.

Just think about it for a moment: One gram of DNA can store 700 terabytes of data. That’s 14,000 50-gigabyte Blu-ray discs… in a droplet of DNA that would fit on the tip of your pinky. To store the same kind of data on hard drives — the densest storage medium in use today — you’d need 233 3TB drives, weighing a total of 151 kilos. In Church and Kosuri’s case, they have successfully stored around 700 kilobytes of data in DNA — Church’s latest book, in fact — and proceeded to make 70 billion copies (which they claim, jokingly, makes it the best-selling book of all time!) totaling 44 petabytes of data stored.

Looking forward, they foresee a world where biological storage would allow us to record anything and everything without reservation. Today, we wouldn’t dream of blanketing every square meter of Earth with cameras, and recording every moment for all eternity/human posterity — we simply don’t have the storage capacity. There is a reason that backed up data is usually only kept for a few weeks or months — it just isn’t feasible to have warehouses full of hard drives, which could fail at any time. If the entirety of human knowledge — every book, uttered word, and funny cat video — can be stored in a few hundred kilos of DNA, though… well, it might just be possible to record everything (hello, police state!)

It’s also worth noting that it’s possible to store data in the DNA of living cells — though only for a short time. Storing data in your skin would be a fantastic way of transferring data securely…

Thank the gods that we’ll finally be able to save all of those Youtube videos of cats acting all cute for future generations to gush over. I can rest easy knowing that some of the greatest accomplishments of scientific minds will be squandered away on trivial passtimes.

~ ~ ~

Living organ-on-a-chip could soon replace animal testing

If a team of Harvard bioengineers has its way, animal testing and experimentation could soon be replaced by organ-on-a-chip technologies. Like SoCs (system-on-a-chip), which shoehorn most of a digital computer into a single chip, an organ-on-a-chip seeks to replicate the functions of a human organ on a computer chip.

In Harvard’s case, its Wyss Institute has now created a living lung-on-a-chip, a heart-on-a-chip, and most recently a gut-on-a-chip.

We’re not talking about silicon chips simulating the functions of various human organs, either. These organs-on-a-chip contain real, living human cells. In the case of the gut-on-a-chip, a single layer of human intestinal cells is coerced into growing on a flexible, porous membrane, which is attached to the clear plastic walls of the chip. By applying a vacuum pump, the membrane stretches and recoils, just like a human gut going through the motions of peristalsis. It is so close to the real thing that the gut-on-a-chip even supports the growth of living microbes on its surface, like a real human intestine.

In another example, the Wyss Institute has built a lung-on-a-chip, which has human lung cells on the top, a membrane in the middle, and blood capillary cells beneath. Air flows over the top, while real human blood flows below. Again, a vacuum pump makes the lung-on-a-chip expand and contract, like a human lung.

These chips are also quite closely tied to the recent emergence of the lab-on-a-chip (LoC), which combines microfluidics (exact control of tiny amounts of fluid) and silicon technology to massively speed up the analysis of biological systems, such as DNA. It is thanks to LoCs that we can sequence entire genomes in just a few hours — a task that previously took weeks or months.

These human organs-on-a-chip can be tested just like a human subject — and the fact that they’re completely transparent is obviously a rather large boon for observation, too. To test a drug, the researchers simply add a solution of the compound to the chip, and see how the intestinal (or heart or lung) cells react. In the case of the lung-on-a-chip, the Wyss team is testing how the lung reacts to possible toxins and pollutants. They can also see how fast drugs (or foods) are absorbed, or test the effects of probiotics.

Perhaps more importantly, these chips could help us better understand and treat diseases. Many human diseases don’t have an animal analog. It’s very hard to find a drug that combats Crohn’s disease when you can’t effectively test out your drug on animals beforehand — a problem that could be easily solved with the gut-on-a-chip. Likewise, it is very common for drugs to pass animal testing, but then fail on humans. Removing animal testing from the equation would save money and time, and also alleviate any ethical concerns.

Moving forward, the Wyss Institute, with funding from DARPA, is currently researching a spleen-on-a-chip. This won’t be used for pharmaceutical purposes, though; instead, DARPA wants to create a “portable spleen” that can be inserted into soldiers to help battle sepsis (an infection of the blood).

And therein lies the crux: If you can create a chip that perfectly mimics the spleen or liver or intestine, then what’s to stop you from inserting those chips into humans and replacing or augmenting your current organs? Instead of getting your breasts enlarged, you might one day have your liver enlarged, to better deal with your alcoholism. Or how we connect all the organ chips together and create a complete human-on-a-chip?

118 Days to Dec 21st 2012


First “successfully” Genetically Modified Humans [tm]

29 June 2012

Even a slippery slope can take all the fun out of sex.

I keep expecting to see this in the Onion, and if it is a joke, it is decidedly unfunny. After modifying the genetics of animals and plants, and feeding them to animals and humans, this was the next step. I can’t wait until humans are modified to be tolerant to pesticides and GMOs, so that we never have to revisit the foolhardiness of industrialized agriculture.

In terms of human reproduction, I have wondered why we don’t take infertility as a symptom of a much bigger problem (human bodies full of pesticides, for example), and instead of treating the cause (i.e. cleaning up where we live), we continue to treat the symptoms. If you can’t have babies, it is the surest sign that you shouldn’t have babies.

World’s First GM Babies Born

The world’s first geneticallymodified humans have been created, it was revealed last night.

The disclosure that 30 healthy babies were born after a series of experiments in the United States provoked another furious debate about ethics.

So far, two of the babies have been tested and have been found to contain genes from three ‘parents’.

Fifteen of the children were born in the past three years as a result of one experimental programme at the Institute for Reproductive Medicine and Science of St Barnabas in New Jersey.

The babies were born to women who had problems conceiving. Extra genes from a female donor were inserted into their eggs before they were fertilised in an attempt to enable them to conceive.

Genetic fingerprint tests on two one-year- old children confirm that they have inherited DNA from three adults –two women and one man.

The fact that the children have inherited the extra genes and incorporated them into their ‘germline’ means that they will, in turn, be able to pass them on to their own offspring.

Altering the human germline – in effect tinkering with the very make-up of our species – is a technique shunned by the vast majority of the world’s scientists.

Geneticists fear that one day this method could be used to create new races of humans with extra, desired characteristics such as strength or high intelligence.

Writing in the journal Human Reproduction, the researchers, led by fertility pioneer Professor Jacques Cohen, say that this ‘is the first case of human germline genetic modification resulting in normal healthy children’.

Some experts severely criticised the experiments. Lord Winston, of the Hammersmith Hospital in West London, told the BBC yesterday: ‘Regarding the treat-ment of the infertile, there is no evidence that this technique is worth doing . . . I am very surprised that it was even carried out at this stage. It would certainly not be allowed in Britain.’

John Smeaton, national director of the Society for the Protection of Unborn Children, said: ‘One has tremendous sympathy for couples who suffer infertility problems. But this seems to be a further illustration of the fact that the whole process of in vitro fertilisation as a means of conceiving babies leads to babies being regarded as objects on a production line.

‘It is a further and very worrying step down the wrong road for humanity.’ Professor Cohen and his colleagues diagnosed that the women were infertile because they had defects in tiny structures in their egg cells, called mitochondria.

They took eggs from donors and, using a fine needle, sucked some of the internal material – containing ‘healthy’ mitochondria – and injected it into eggs from the women wanting to conceive.

Because mitochondria contain genes, the babies resulting from the treatment have inherited DNA from both women. These genes can now be passed down the germline along the maternal line.

A spokesman for the Human Fertilisation and Embryology Authority (HFEA), which regulates ‘assisted reproduction’ technology in Britain, said that it would not license the technique here because it involved altering the germline.

Jacques Cohen is regarded as a brilliant but controversial scientist who has pushed the boundaries of assisted reproduction technologies.

He developed a technique which allows infertile men to have their own children, by injecting sperm DNA straight into the egg in the lab.

Prior to this, only infertile women were able to conceive using IVF. Last year, Professor Cohen said that his expertise would allow him to clone children –a prospect treated with horror by the mainstream scientific community.

‘It would be an afternoon’s work for one of my students,’ he said, adding that he had been approached by ‘at least three’ individuals wishing to create a cloned child, but had turned down their requests.

175 Days to Dec 21st 2012


Cycles of Time – Becoming the Body

16 February 2012

looking at time systems from the small to the all

Previous posts on these subjects:

Maya 13 Baktun – each column is 394 years from 3113 BC – 2012 CE

When referring to fractals of time, I mean to say the self-similar aspect of fractals. In the Long Count Calendar of Mesoamerica (the Maya, Aztec and others), uses units of 20 to organize their day count. There are periods of 20 days, similar to a month. 18 of those is a vague year (360 days). This vague year is called a tun. 20 tun, then 20 x 20 tun, then 20 x 20 x 20 tun and so on. The other number that is key to the timekeeping system of Mesoamerica is 13. Thus 13 x 20 = 260 is a doubly important number. 260 days is the length of their sacred calendar; 260 katun is the length of the period of history coming to an end on December 21st 2012 CE.

Although for us, the year is important for longer periods of time. Something I stumbled across was the period between three key years in calendar history: 1492 Europeans discovered the peoples of the Americas, bringing the Julian and Mesoamerican perspective on time together. 260 years later, 1752, the British Empire switched from the Julian to the Gregorian Calendar, making it the most widespread calendar in use in the world. 260 years later, 2012, the end of the Long Count Calendar’s 13 baktun, or 260 katun period. Does it mean anything? Only what you want it to.

fractal patterns display self-similarity across scale

Fractals aren’t theoretical, they appear throughout nature, like in Romanesco broccoli.

Two archaic films (both from 1968) used the zoom to get across the scales of existence from the tiny to the enormous.

Beyond Numbers – Our Body in Time

This experiment in time is an exercise in developing our health, believe it or not (or at least give it a think). In several traditional medicines, diagnoses are made by looking at the face, the feet and other body parts as maps to the entire body. If there is a lesion in a particular spot, it tells of a deeper problem elsewhere.

If time is a matter of perception, as with colour, flavour, sound, sensation and so forth, then our understanding of it on a cosmic scale is completely dependent of us understanding it on a personal scale.

The 260-day cycle that the Maya use for their sacred calendar was original derived from the particular location where it was developed (by another culture on the Pacific Coast of Mexico). The Sun would pass directly overhead at its highest point in April, then slowly move its way South (to the Tropic of Capricorn), then return on August 13th. This would take 260 days. However, more recently, the 260 days have been tied to the length of human gestation. We currently round gestation off to 9 lunar months or 266 days. Using the gestation period as the foundation of a fractal timekeeping system is insightful. It ties our first experience of time as our very body develops to those of the cycles of the cosmos.

For the first 13 days of gestation, the cell (zygote) divides into 2, then 4, 8 and so on until it reaches 64 or 128 cells. Throughout this stage, the ball of cells is called a  morula Then something miraculous happens: gastrulation. The cells differentiate into three membranes which will develop into all of our tissues and organs: the ectoderm (which will become the skin and nervous system), the endoderm (which will become the digestive and respiratory systems), and the mesoderm (which will become the muscle and skeletal systems).

Traditional Ayurvedic Medicine uses these membranes (called doshas) as the basis for diet, health and well being. Ayurveda and Traditional Chinese Medicine both use symbology to tie the body to the greater social and cosmic cycles, through the use of the 5 elements, yin-Yang and other associated qualities. The difficulty I have with our very young tradition of scientific medicine is that it is so complex in its detail that there are numerous specialized fields, which leaves the layman further removed from sharing our cultural knowledge of how we regard our bodies and health, and many settle for the quackery of television and tabloid generalizations.

Prostrating before the masses.

Although our personal development begins with conception (I refuse to enter the debate on when life begins. My answer is 4 billion years ago), the process began long before, with our parents, their parents and so on, and on the molecular level, with their DNA. DNA as the basis of all life and reproduction (well, RNA as well), it is an important consideration.

DNA molecules are being developed into molecular computers, although this is still in the early stages. Bases pair up with each other, forming the rungs of the ladder in the animation above. There are 4 bases, two pairing types: adenine (A) forms a base pair with thymine (T) and guanine (G) forms a base pair with cytosine (C). In RNA, thymine is replaced by uracil (U).

Three consecutive bases form a codon, which defines the amino acid/protein to be developed in the cell. There are 20 amino acids defined by 64 codons. I’m not trying to get too deeply into molecular biology (which I always struggled with) or genetics (which I struggled with only slightly less), but at least want to look at the basis of life, and the basic math we associate with it. This has been done before, as I have previously posted about, by the folks at the 13 moon law of time site, founded by Jose Arguelles.

In the above graphic, the tao and I ching binary system links the 64 hexagrams with the 64 codons.

The Maya also held 20 as sacred, likely because it is our total number of digits (fingers and toes). It’s also the number of amino acids.

By the Numbers

What are the time periods most fundamental to us in terms of natural timekeeping? The Day, Lunation and Year are the foundation. Joseph Campbell associated the second with the resting adult heart rate, which if you’re going to build an arbitrary time system seems as good a starting point as ever. In Ayurveda, blinking and the breath are tied to 4 second periods. These are by no means measure of an actual breath, or an actual heart rate, but Platonic ideals, not as some idea of perfection to strive for, but as a symbolic number to tie things together. A mnemonic. It is more effective to have a system in place than to go with rote memorization.

Binary

The I Ching and tao use a binary counting system. As it’s the basis for computer language, it seems appropriate that we should become more familiar with it. However, our approach to binary thought in North America is divisive, whereas the taoist is complimentary.

We tend to see extremes as conflicting opposites. Light-Dark are seen as forces of good and evil. One is expected to align themselves with the good and oppose the evil. This creates a rift between the extremes. Light is good, dark evil. The taoist view is that the extremes define the space between them. Light and dark are polar perfections, and we exist in the interplay of grey, shade, shadow, red, green, indigo and all variation in between.

There is a progression from the absence (as with dark, or cold) to presence (light, heat). The in-between is the gradation. Both extremes are necessary, and opposing one in favour of the other brings imbalance. At least, that’s my dilettantish opinion on the matter.

The binary system reflects our first physical days, dividing from one zygote to 2 cells, 4 cells, 8, 16, 32, 64, 128 through the process of mitosis. It is the basis of the I ching which is also tied to time, the moon, the seasons. It is an essential link.

Three

The three embryonic membranes determine all of our body tissues. We perceive three primary hues of colour. Our sense of space is defined by three dimensions, in no small part due to the three semi-circular canals in the inner ear which determine our balance. Three bases form a codon.These are a few fundamental biological examples of 3. There are more.

Four

Our DNA/RNA have four base pairs, we have four limbs, our hearts have four chambers, our livers have four lobes.

Five

One way of defining 5 is 4 + 1 (my thanks to grade 1 math). 5 base pairs – DNA uses four, RNA uses a different set of four. Four limbs, but 5 extremities, if we count our head. Our two lungs have 5 lobes. We have 5 digits per limb. We can think of 10 and 20 as multiples of 5.

Nine

Human gestation lasts 9 lunar months.

Thirteen

We have 13 major articulations (neck, shoulders, elbows, wrists, hips, knees, ankles).

Conclusion

For the moment, it appears that the traditional Chinese, Indian and Mesoamerican systems of timekeeping might harmonize the levels of time best. These at least represent the East Asia, Southeast Asia, the Americas. Not to exclude others, by any means. Scientific astronomy, medicine and so forth will certainly play a role, but the essence of this is in its coherence, and self-similarity.

I am not above fudging numbers for the sake of a beautifying the system. =)

309 Days to Dec 21st 2012


Tying together time and Genetics

12 January 2012

How do codons and calends combine?

Supercoiling

Supercoiling is a means for long strands (typically referring to DNA, as in the video below) to coil into dense packages, as opposed to remaining as one long linear ribbon (see also ribbon theory & knot theory).

Imagine that each day were a pearl on a long string. 365 pearls would be a year-long necklace, if you follow me. Now picture coiling up those 365 pearls into 28-pearl coils. And then each of those into 7-pearl coils. You’d have 7 coils within 4 coils within 13 coils.

In a sense, this pattern of coiling is similar to the path described by planetary and lunar orbits – the moon orbits the earth (kind of), the earth orbits the sun, the sun orbits Sag A* (the black hole at the centre of the milky way). You could picture the path of the moon’s orbit as a coiling around the earth as it coils around the Sun as it coils around the milky way. Just trying to find a visual means of representing time through supercoiling (and if I knew how to animate it online, I would do so, but I don’t, so I haven’t).

This is a means of visualizing self-similar aspects of time, as described in yesterday’s post.

For the moment, let’s just consider the relationship between DNA and time:

This was taken from the law of time site, and I can’t find the original. Apologies.

In the mandala above, the artist has linked the 64 hexagrams of the I Ching to the 64 codons of RNA – the codons are defined by 3 consecutive base pairs (the building block molecules of our genetic material). There are 4 bases (Adenine, Guanine, Cystosine and Uracil) which are abbreviated A, G, C, U respectively. A codon can be any 3 of these AAA, AAG, AAC, etc… through to UUU. This gives us a total of 64 different codons. Each codon specifies a particular amino acid (or stop/start signal) that is added in the protein synthesis stage.

This ties DNA to the I Ching which in turn is connected to the reckoning of time (not to mention DNA computing). Considering our genetic material is what allows us to reproduce as a species, it is inherently tied to time in terms of successive generations (which I arbitrarily assign at 20 years). At any rate, there is more to be explored here, but for the time being, let’s just leave it at these superficial similarities.

Let us also not forget Dr David Deamer (et al) and their work using proteins & DNA sequences to create music based on molecular structure.

Knotworks

While we’re talking about superstrings, supercoils and other super things, why not knots? The Inca, who had a time system build into their landscape, also used a system of knotted strings to communicate, called the Quipu.

It’s an elaborate system, but nevertheless speaks of human ingenuity when it comes to communication. Oh, what a tangled web we weave and so on. This is reminiscent (to me anyway) of the wampum used by the Natives of the Eastern Woodlands of North America,  which uses beads made of channeled whelk and quahog shells as opposed to knots to communicate.

These are both ingenious methods of weaving meaning into art. Which might well serve us when designing a meaningful system of time-reckoning.